Transcription factor Affinity Prediction

Determines the total affinity of a sequence for a given transcription factor, thus removing the need for a threshold value. TRAP ranks all promoter sequences of a genome on the basis of their overall affinity for that factor to proceed. It can serve to estimate the most enriched factor into a given sequence, the sequences with the highest affinity for a factor of interest, or the binding sites of a factor affected by the given single nucleotide polymorphisms (SNPs).

Investigation of single and synergic effects of NLRC5 and PD L1 variants on the risk of colorectal cancer

[…] nvestigate the 3’-UTR and to predict if a SNP within the target site will disrupt/eliminate or enhance/create a microRNA binding site. PERFECTOS-APE (http://opera.autosome.ru/perfectosape/scan) and s-Transcription factor Affinity Prediction (s-TRAP, http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) were used to identify transcription factors whose binding sites can be significantly affected […]

[…] ah (CEU) population []. The r2 was 80% and the distance limit was 500 kb. GWAS catalog was then used to verify if tagged and non-tagged SNPs have been previously identified in a GWAS []. Finally, the Transcription factor Affinity Prediction (TRAP) web tool for two sequences was used to evaluate transcription factor binding affinity differences between the alleles of tagged SNPs [,,]. […]

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Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans

2017

Int J Mol Sci

PMCID: 5343793

PMID: 28134766

DOI: 10.3390/ijms18020257

[…] using SNP Annotation and Proxy Search (SNAP) with an r2 threshold of 0.8 and a distance limit of 500 kb []. LD was calculated with the Northern Europeans from Utah (CEU) population. We also used the Transcription factor Affinity Prediction (TRAP) web tools for single sequences to measure the possible transcription factor binding affinities to tagged SNP regions in the presence or absence of SNPs […]

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Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

[…] dules downregulated (modules 5–9), or containing similarly expressed genes across conditions (module 10), were enriched in functions such as RNA processing and translational termination (B).Using the transcription factor affinity prediction (TRAP) method (), we found that the annotated promoter regions of the genes within each module were enriched in binding motifs for specific transcription facto […]

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In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences

2016

Sci Rep

PMCID: 5007594

PMID: 27582178

DOI: 10.1038/srep32476

[…] (PWM). In this work, a total of 1,422 PWMs were collected from Cistrome and the TRANSFAC track in the UCSC Genome Browser. For a given sequence, the ability of a TF to bind DNA was represented by the transcription factor affinity prediction (TRAP) score, which was calculated according to the transcription factor motif PWM by the TRAP program. The parameters of the TRAP program used default values. […]

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Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation

[…] http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3. The searching result of potential TFBS will be displayed through a graphical interface or as a downloadable text file. (3) Transcription factor affinity prediction (TRAP): TRAP is used to predict which TFs are susceptible to bind a promoter with highest affinity. TRAP uses the TRANSFAC database and the searching result is […]